SMTL ID : 9cmf.1

Substrate bound DosP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 14 residues within 4Å: Chain A: I.17, I.50, P.51, L.54, H.58, N.65, R.78, L.80, Q.81, L.82, F.94, L.96, Y.107 Ligands: OXY.2 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:I.17, A:I.50, A:L.54, A:N.65, A:L.80, A:L.82, A:F.94, A:L.96, A:Y.107 Hydrogen bonds: A:N.65 Salt bridges: A:K.70, A:R.78 pi-Cation interactions: A:R.78 HEM.6: 16 residues within 4Å: Chain B: I.17, I.50, P.51, L.54, H.58, Y.61, H.64, N.65, K.70, M.76, R.78, Q.81, L.82, L.96, Y.107 Ligands: OXY.7 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:I.17, B:I.50, B:Y.61, B:L.82, B:L.96, B:Y.107, B:Y.107 Salt bridges: B:H.64, B:K.70, B:R.78 pi-Cation interactions: B:R.78 Metal complexes: B:H.58

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 3 residues within 4Å: Chain A: R.78, L.96 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.78 OXY.7: 4 residues within 4Å: Chain B: R.78, L.80, F.94 Ligands: HEM.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.78, B:R.78

2 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.3: 15 residues within 4Å: Chain A: Q.551, E.565, L.567, A.568, R.569, P.580, V.600, N.624, K.710, G.744, V.745, G.764, Y.765 Ligands: MG.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.551, A:E.565, A:A.568, A:R.569, A:N.624, A:N.624, A:Y.765, A:Y.765 Salt bridges: A:R.569, A:E.746 pi-Stacking: A:Y.765 pi-Cation interactions: A:Y.765 C2E.8: 15 residues within 4Å: Chain B: Q.551, E.565, L.567, A.568, R.569, P.580, V.600, N.624, E.743, G.744, V.745, G.764, Y.765 Ligands: MG.9, MG.10 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.551, B:A.568, B:R.569, B:N.624, B:N.624, B:G.744, B:Y.765 Salt bridges: B:R.569, B:E.746 pi-Stacking: B:Y.765 pi-Cation interactions: B:Y.765

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.565, N.624 Ligands: C2E.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: C2E.3 MG.5: 3 residues within 4Å: Chain A: D.686, D.709 Ligands: C2E.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.686 MG.9: 5 residues within 4Å: Chain B: E.565, N.624, K.707, E.743 Ligands: C2E.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.565, C2E.8 MG.10: 3 residues within 4Å: Chain B: D.686, E.743 Ligands: C2E.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.686, B:E.743, C2E.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, W. et al., Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain. Nat Commun (2024)

Release Date

2024-11-20

Peptides

Oxygen sensor protein DosP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oxygen sensor protein DosP